Atrial fibrillation - Heart Left Ventricle
sheng Qian
2021-12-18
Last updated: 2022-02-11
Checks: 6 1
Knit directory: cTWAS_analysis/
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Weight QC
[1] 10150
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1003 711 570 412 451 607 495 367 384 411 592 556 186 332 344 494
17 18 19 20 21 22
639 150 783 300 110 253 [1] 6644[1] 0.6545813Load ctwas results
Check convergence of parameters
********************************************************Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute:
theme_set(theme_cowplot())********************************************************
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
gene snp
0.0196935664 0.0002083061 gene snp
9.374271 8.577991 [1] 1030836[1] 10150 6839050 gene snp
0.001817768 0.011854791 [1] 0.01188393 0.13624409Genes with highest PIPs
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
genename region_tag susie_pip mu2 PVE z num_eqtl
3169 PRRX1 1_84 0.9999999 153.79916 1.491985e-04 14.848088 2
3147 WIPF1 2_105 0.9993101 2124.21550 2.059251e-03 8.987351 2
2431 DNAJC12 10_44 0.9967458 850.85693 8.227187e-04 -5.328244 1
1214 GMCL1 2_46 0.9944249 60.60721 5.846645e-05 -8.434995 2
9840 NKX2-5 5_103 0.9942183 61.83714 5.964054e-05 -9.616279 2
10979 MSRB1 16_2 0.9667967 26.84161 2.517411e-05 5.929412 1
9417 PLEC 8_94 0.9666163 43.61991 4.090245e-05 3.093844 2
6663 JAM2 21_9 0.9633616 22.37976 2.091487e-05 4.569598 2
7794 KDM1B 6_14 0.9581444 64.33734 5.980046e-05 -9.000000 1
2987 GNB4 3_110 0.9537748 32.01351 2.962031e-05 -5.869048 1
11279 DPF3 14_34 0.9246749 30.95765 2.776946e-05 6.100000 1
2960 PCCB 3_84 0.9229236 849.82984 7.608659e-04 -5.382353 1
9960 PGP 16_2 0.9051693 28.48915 2.501611e-05 5.943820 1
1551 CCDC134 22_17 0.8683170 26.15261 2.202945e-05 -5.180556 1
12376 LINC01314 15_37 0.8300211 20.71969 1.668334e-05 -4.379164 4
4891 NPL 1_90 0.8251030 18.75569 1.501245e-05 -3.825175 1
5042 PSMB7 9_64 0.8211676 25.19921 2.007378e-05 -4.820896 1
8847 WASHC2C 10_31 0.8186904 19.80281 1.572740e-05 -3.972152 1
12133 LINC00964 8_82 0.8180590 22.20129 1.761867e-05 4.554265 2
3725 SSPN 12_18 0.7969230 42.42202 3.279579e-05 -6.791667 1Genes with largest effect sizes
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
genename region_tag susie_pip mu2 PVE z
3147 WIPF1 2_105 0.9993100519 2124.2155 2.059251e-03 8.987351
929 BAZ2A 12_35 0.0000000000 1327.6344 0.000000e+00 -5.942857
10471 ZNF292 6_59 0.0000000000 1098.8945 0.000000e+00 -5.216216
4819 CGA 6_59 0.0000000000 912.8138 0.000000e+00 4.780822
7442 GPR155 2_105 0.0000000000 887.5060 0.000000e+00 -4.929575
2431 DNAJC12 10_44 0.9967457594 850.8569 8.227187e-04 -5.328244
2960 PCCB 3_84 0.9229235511 849.8298 7.608659e-04 -5.382353
6231 HERC4 10_44 0.0519716850 784.1117 3.953258e-05 -5.368895
7690 SLC35A1 6_59 0.0000000000 731.3839 0.000000e+00 -4.906053
4816 ORC3 6_59 0.0000000000 575.4343 0.000000e+00 -4.305556
11646 AC010894.3 2_105 0.0000000000 567.5177 0.000000e+00 2.807292
2445 WNT3 17_28 0.0012204211 558.1877 6.608462e-07 -5.270588
10151 ARL17A 17_28 0.0006810977 537.9069 3.554078e-07 -4.159800
10265 MAPT 17_28 0.0246154818 498.1750 1.189599e-05 5.606451
5236 MYPN 10_44 0.0557487640 467.4182 2.527850e-05 4.754237
11600 MKRN2OS 3_9 0.0000000000 326.2847 0.000000e+00 -2.927621
1450 SIRT1 10_44 0.0073685535 237.7219 1.699268e-06 -2.641975
856 PPP2R3A 3_84 0.0000000000 231.0518 0.000000e+00 -2.690141
8296 PDHB 3_40 0.0160173130 201.8814 3.136869e-06 2.296671
11694 ARL17B 17_28 0.0028320351 185.4496 5.094893e-07 3.095544
num_eqtl
3147 2
929 1
10471 1
4819 1
7442 3
2431 1
2960 1
6231 2
7690 2
4816 1
11646 2
2445 1
10151 2
10265 2
5236 1
11600 2
1450 1
856 1
8296 2
11694 2Genes with highest PVE
genename region_tag susie_pip mu2 PVE z
3147 WIPF1 2_105 0.99931005 2124.21550 2.059251e-03 8.987351
2431 DNAJC12 10_44 0.99674576 850.85693 8.227187e-04 -5.328244
2960 PCCB 3_84 0.92292355 849.82984 7.608659e-04 -5.382353
3169 PRRX1 1_84 0.99999992 153.79916 1.491985e-04 14.848088
11458 ZSWIM8 10_49 0.72951933 109.78862 7.769705e-05 -11.216495
7794 KDM1B 6_14 0.95814438 64.33734 5.980046e-05 -9.000000
9840 NKX2-5 5_103 0.99421828 61.83714 5.964054e-05 -9.616279
1214 GMCL1 2_46 0.99442495 60.60721 5.846645e-05 -8.434995
9417 PLEC 8_94 0.96661634 43.61991 4.090245e-05 3.093844
6231 HERC4 10_44 0.05197169 784.11168 3.953258e-05 -5.368895
2927 NR3C1 5_84 0.79565655 45.98656 3.549498e-05 -8.392405
3725 SSPN 12_18 0.79692298 42.42202 3.279579e-05 -6.791667
2987 GNB4 3_110 0.95377479 32.01351 2.962031e-05 -5.869048
11279 DPF3 14_34 0.92467491 30.95765 2.776946e-05 6.100000
3396 CASQ2 1_72 0.64365572 44.46248 2.776244e-05 6.684932
2401 PITX3 10_65 0.70424642 39.87615 2.724258e-05 -6.793786
5236 MYPN 10_44 0.05574876 467.41822 2.527850e-05 4.754237
10979 MSRB1 16_2 0.96679672 26.84161 2.517411e-05 5.929412
9960 PGP 16_2 0.90516927 28.48915 2.501611e-05 5.943820
1551 CCDC134 22_17 0.86831704 26.15261 2.202945e-05 -5.180556
num_eqtl
3147 2
2431 1
2960 1
3169 2
11458 1
7794 1
9840 2
1214 2
9417 2
6231 2
2927 1
3725 1
2987 1
11279 1
3396 1
2401 2
5236 1
10979 1
9960 1
1551 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z
3169 PRRX1 1_84 9.999999e-01 153.79916 1.491985e-04 14.848088
7976 SYNPO2L 10_48 1.466304e-01 134.47936 1.912890e-05 -11.782609
11458 ZSWIM8 10_49 7.295193e-01 109.78862 7.769705e-05 -11.216495
7134 ZBTB7B 1_76 1.008001e-04 120.87046 1.181930e-08 10.638889
504 SYNE2 14_29 4.741777e-02 83.62062 3.846492e-06 10.029851
9840 NKX2-5 5_103 9.942183e-01 61.83714 5.964054e-05 -9.616279
7794 KDM1B 6_14 9.581444e-01 64.33734 5.980046e-05 -9.000000
3147 WIPF1 2_105 9.993101e-01 2124.21550 2.059251e-03 8.987351
3876 DEK 6_14 9.860627e-02 62.21941 5.951697e-06 -8.651764
1214 GMCL1 2_46 9.944249e-01 60.60721 5.846645e-05 -8.434995
7445 DCST2 1_76 6.958988e-04 82.23437 5.551494e-08 -8.408993
2927 NR3C1 5_84 7.956566e-01 45.98656 3.549498e-05 -8.392405
9371 MYOZ1 10_48 4.594225e-02 72.94692 3.251095e-06 8.282302
5279 HCN4 15_35 1.027118e-03 142.65541 1.421409e-07 7.582677
554 MXD1 2_46 5.931507e-02 49.69584 2.859536e-06 7.537313
2039 ASAH1 8_21 2.248119e-05 67.20598 1.465675e-09 -7.443420
2401 PITX3 10_65 7.042464e-01 39.87615 2.724258e-05 -6.793786
3725 SSPN 12_18 7.969230e-01 42.42202 3.279579e-05 -6.791667
7823 CFL2 14_9 2.408814e-02 112.05711 2.618504e-06 -6.728039
5803 ADAM15 1_76 7.026909e-04 51.73422 3.526571e-08 -6.717647
num_eqtl
3169 2
7976 1
11458 1
7134 1
504 1
9840 2
7794 1
3147 2
3876 3
1214 2
7445 2
2927 1
9371 2
5279 1
554 1
2039 2
2401 2
3725 1
7823 2
5803 1Comparing z scores and PIPs
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
[1] 0.007783251 genename region_tag susie_pip mu2 PVE z
3169 PRRX1 1_84 9.999999e-01 153.79916 1.491985e-04 14.848088
7976 SYNPO2L 10_48 1.466304e-01 134.47936 1.912890e-05 -11.782609
11458 ZSWIM8 10_49 7.295193e-01 109.78862 7.769705e-05 -11.216495
7134 ZBTB7B 1_76 1.008001e-04 120.87046 1.181930e-08 10.638889
504 SYNE2 14_29 4.741777e-02 83.62062 3.846492e-06 10.029851
9840 NKX2-5 5_103 9.942183e-01 61.83714 5.964054e-05 -9.616279
7794 KDM1B 6_14 9.581444e-01 64.33734 5.980046e-05 -9.000000
3147 WIPF1 2_105 9.993101e-01 2124.21550 2.059251e-03 8.987351
3876 DEK 6_14 9.860627e-02 62.21941 5.951697e-06 -8.651764
1214 GMCL1 2_46 9.944249e-01 60.60721 5.846645e-05 -8.434995
7445 DCST2 1_76 6.958988e-04 82.23437 5.551494e-08 -8.408993
2927 NR3C1 5_84 7.956566e-01 45.98656 3.549498e-05 -8.392405
9371 MYOZ1 10_48 4.594225e-02 72.94692 3.251095e-06 8.282302
5279 HCN4 15_35 1.027118e-03 142.65541 1.421409e-07 7.582677
554 MXD1 2_46 5.931507e-02 49.69584 2.859536e-06 7.537313
2039 ASAH1 8_21 2.248119e-05 67.20598 1.465675e-09 -7.443420
2401 PITX3 10_65 7.042464e-01 39.87615 2.724258e-05 -6.793786
3725 SSPN 12_18 7.969230e-01 42.42202 3.279579e-05 -6.791667
7823 CFL2 14_9 2.408814e-02 112.05711 2.618504e-06 -6.728039
5803 ADAM15 1_76 7.026909e-04 51.73422 3.526571e-08 -6.717647
num_eqtl
3169 2
7976 1
11458 1
7134 1
504 1
9840 2
7794 1
3147 2
3876 3
1214 2
7445 2
2927 1
9371 2
5279 1
554 1
2039 2
2401 2
3725 1
7823 2
5803 1SNPs with highest PIPs
id region_tag susie_pip mu2 PVE z
28637 rs12404927 1_75 1.0000000 1404.55102 1.362536e-03 -1.5517241
28638 rs7536152 1_75 1.0000000 1439.64649 1.396582e-03 -6.4626866
28731 rs34515871 1_76 1.0000000 296.98405 2.881002e-04 17.0000000
32608 rs12142529 1_83 1.0000000 145.38857 1.410395e-04 12.0396040
32633 rs112797273 1_83 1.0000000 101.40197 9.836867e-05 9.4903846
183948 rs1906615 4_72 1.0000000 3299.17745 3.200487e-03 45.1604938
183953 rs7440714 4_72 1.0000000 1498.40640 1.453584e-03 -9.2183406
272791 rs111990232 6_59 1.0000000 1672.21316 1.622191e-03 0.5392670
472755 rs17287293 12_18 1.0000000 150.43066 1.459307e-04 -10.2947368
556238 rs140798119 15_35 1.0000000 282.62226 2.741680e-04 3.9950739
556241 rs74022964 15_35 1.0000000 340.33003 3.301495e-04 12.5777778
698783 rs4972703 2_105 1.0000000 3592.88497 3.485409e-03 -0.7842670
703489 rs114415025 3_9 1.0000000 2723.92507 2.642443e-03 1.2192513
728978 rs201862093 7_48 1.0000000 1114.36488 1.081030e-03 -0.8625000
765251 rs76106073 10_44 1.0000000 836.85538 8.118220e-04 0.6572238
768375 rs61937778 12_35 1.0000000 1898.73730 1.841939e-03 -1.3056995
28735 rs2878412 1_76 1.0000000 104.66388 1.015330e-04 5.4250000
423415 rs60469668 10_66 1.0000000 171.39264 1.662657e-04 16.9647059
28733 rs11576820 1_76 1.0000000 131.66128 1.277228e-04 8.0243902
592256 rs62056842 17_28 1.0000000 764.07813 7.412218e-04 1.1269036
733889 rs62643683 8_21 1.0000000 262.98617 2.551193e-04 0.8007519
183979 rs186546224 4_72 1.0000000 278.28019 2.699558e-04 -6.8398876
117614 rs7373492 3_28 1.0000000 57.12050 5.541183e-05 -7.6417323
323213 rs62469005 7_70 1.0000000 248.90606 2.414604e-04 -3.8636364
323204 rs28557111 7_70 0.9999995 268.50949 2.604773e-04 13.6818182
299063 rs12112152 7_15 0.9999995 45.05583 4.370803e-05 6.9358974
28738 rs10908445 1_76 0.9999993 192.70836 1.869436e-04 -13.1470588
576584 rs6499606 16_39 0.9999989 103.66865 1.005674e-04 12.6376812
785055 rs8005417 14_9 0.9999977 418.17010 4.056602e-04 0.9863946
323219 rs12669209 7_70 0.9999965 107.24435 1.040359e-04 -4.2937500
423413 rs7094488 10_66 0.9999961 105.12014 1.019752e-04 14.1060606
96493 rs1975584 2_118 0.9999837 71.18500 6.905447e-05 1.2311828
804323 rs140185678 16_2 0.9999825 44.60953 4.327434e-05 7.6100917
280210 rs11756438 6_79 0.9999688 47.48500 4.606312e-05 -8.2089552
117485 rs116202356 3_27 0.9999532 36.40320 3.531260e-05 6.0813559
176633 rs1458038 4_54 0.9998799 34.94748 3.389801e-05 6.0277778
661464 rs464901 22_3 0.9997751 44.32757 4.299190e-05 -7.0555556
121514 rs12330500 3_40 0.9996970 506.36533 4.910693e-04 0.5641026
397657 rs1886296 9_73 0.9995450 34.53850 3.349008e-05 5.9863014
734589 rs7508 8_21 0.9993753 79.71601 7.728312e-05 9.4800000
725018 rs3176326 6_29 0.9991706 50.71157 4.915381e-05 -7.3647059
117627 rs10428132 3_28 0.9991198 74.57949 7.228487e-05 9.2058824
586504 rs72811292 17_11 0.9982520 39.85061 3.859096e-05 -6.5233645
39384 rs12353975 1_102 0.9981456 35.67154 3.454031e-05 -4.3000000
184535 rs7700110 4_73 0.9978791 45.09924 4.365737e-05 7.0666667
117601 rs9824157 3_28 0.9976315 29.97394 2.900844e-05 3.8732394
734231 rs208757 8_21 0.9970887 239.59396 2.317502e-04 7.6629213
232614 rs199992924 5_68 0.9967799 1308.36140 1.265137e-03 -0.6309524
663223 rs133902 22_7 0.9963536 31.00376 2.996666e-05 6.1617647
232434 rs338623 5_68 0.9953355 66.77245 6.447290e-05 -7.9855072
40060 rs4951023 1_104 0.9951712 32.47858 3.135489e-05 5.5970149
39383 rs6427989 1_102 0.9941339 35.76701 3.449355e-05 -4.4142857
592472 rs75230966 17_28 0.9928717 43.15503 4.156569e-05 6.0582524
576592 rs876727 16_39 0.9925728 48.76988 4.695961e-05 -10.0000000
275859 rs9496567 6_67 0.9919760 26.48986 2.549126e-05 5.1125000
801039 rs12908004 15_37 0.9873706 57.56113 5.513405e-05 8.1333333
183968 rs4631108 4_72 0.9858853 278.72914 2.665748e-04 -17.6376812
576597 rs60602157 16_39 0.9858538 38.73318 3.704299e-05 10.4415584
526368 rs74968516 14_8 0.9857359 34.86384 3.333851e-05 -2.0924370
657485 rs7282237 21_16 0.9765780 24.87091 2.356183e-05 -4.7605634
534174 rs2738413 14_29 0.9761605 111.24337 1.053430e-04 -11.6119403
366949 rs7460121 8_88 0.9755516 24.08834 2.279647e-05 4.7500000
323211 rs4730742 7_70 0.9739413 148.25445 1.400719e-04 -5.3181818
576589 rs4788691 16_39 0.9737540 39.90042 3.769096e-05 -1.6900000
331163 rs35760656 7_93 0.9721535 35.73611 3.370176e-05 -6.3536585
284152 rs958747 6_89 0.9716551 24.32337 2.292695e-05 -4.9710145
2727 rs284278 1_7 0.9709039 35.05628 3.301813e-05 -6.0857143
280167 rs77435894 6_78 0.9646884 28.76469 2.691889e-05 6.1111111
785061 rs8011559 14_9 0.9644048 426.28574 3.988142e-04 5.6913580
561807 rs12898337 15_48 0.9627997 35.30067 3.297079e-05 -6.0579710
58545 rs7578482 2_15 0.9603813 32.19728 2.999669e-05 5.7435897
555608 rs745636 15_33 0.9584917 25.47962 2.369146e-05 -5.0740741
25981 rs4839174 1_69 0.9562825 33.83277 3.138588e-05 5.9459459
99263 rs35880620 2_125 0.9544729 39.72780 3.678482e-05 -6.2168675
610855 rs17794590 18_24 0.9544647 24.57014 2.274981e-05 -4.8242424
96468 rs11889306 2_118 0.9532842 45.60961 4.217831e-05 6.7391304
728771 rs74910854 7_48 0.9504108 30.92661 2.851373e-05 5.4878049
705484 rs9830653 3_84 0.9497164 834.68211 7.689985e-04 -0.9344262
784984 rs73241997 14_9 0.9463663 271.39025 2.491517e-04 7.8817204
183920 rs1823291 4_72 0.9443849 275.38267 2.522877e-04 -19.4520548
32655 rs7522387 1_83 0.9380199 59.33695 5.399427e-05 6.6375000
28693 rs906280 1_75 0.9352012 59.46409 5.394737e-05 7.9111111
492885 rs12425471 12_69 0.9315032 41.65186 3.763823e-05 -5.2500000
506242 rs1326122 13_21 0.9280182 24.16457 2.175434e-05 4.7543103
729019 rs112661041 7_48 0.9246584 1098.87113 9.856858e-04 4.6532258
280117 rs89107 6_78 0.9200337 47.40943 4.231350e-05 -9.5606061
372218 rs1594768 9_9 0.9191704 24.06779 2.146064e-05 -4.6911765
218017 rs114414434 5_30 0.9100084 25.52863 2.253634e-05 -4.9718310
416198 rs60632610 10_48 0.9078072 142.32178 1.253359e-04 -12.2395833
5627 rs10917072 1_15 0.9035741 33.32457 2.921048e-05 5.8235294
666612 rs11705586 22_15 0.9032885 25.71531 2.253350e-05 4.8988764
698793 rs1367220 2_105 0.9027873 3624.47361 3.174247e-03 7.2207792
239095 rs6894302 5_84 0.8962639 34.59893 3.008215e-05 -7.2933333
232607 rs4073838 5_68 0.8907151 1336.89003 1.155167e-03 -5.9545455
272788 rs371814 6_59 0.8887549 1684.18630 1.452053e-03 6.1911765
252811 rs73724866 6_13 0.8854526 93.92663 8.067974e-05 -10.4141414
556230 rs519946 15_34 0.8802637 34.42175 2.939383e-05 5.9242424
497493 rs6560886 12_82 0.8786081 28.83992 2.458101e-05 5.6666667
769560 rs71454237 12_43 0.8731783 45.03633 3.814840e-05 -7.3809524
28729 rs12128882 1_76 0.8660530 31.94687 2.684004e-05 1.0731707
469758 rs12821447 12_12 0.8604052 24.28342 2.026858e-05 4.5128205
622090 rs73919353 19_6 0.8573709 29.15094 2.424554e-05 5.4076433
455650 rs565449 11_54 0.8568684 28.25040 2.348276e-05 -5.2535211
67841 rs243080 2_40 0.8464105 23.94966 1.966486e-05 -4.5522388
245279 rs62377226 5_100 0.8419746 33.84803 2.764667e-05 5.8493151
583304 rs75329315 17_2 0.8321222 26.35764 2.127669e-05 -5.2460317
121517 rs6924 3_40 0.8238581 510.02479 4.076187e-04 4.2133333
498623 rs7321083 13_3 0.8169737 24.61195 1.950584e-05 4.8292683
304963 rs145593380 7_26 0.8132918 29.70683 2.343760e-05 5.3333333
151266 rs720389 3_114 0.8068588 23.55072 1.843368e-05 4.2898551SNPs with largest effect sizes
id region_tag susie_pip mu2 PVE z
698793 rs1367220 2_105 9.027873e-01 3624.474 3.174247e-03 7.220779
698794 rs1367219 2_105 8.971134e-02 3615.477 3.146469e-04 7.103896
698789 rs10168156 2_105 2.265398e-01 3615.000 7.944439e-04 7.233766
698787 rs6713018 2_105 5.859132e-02 3613.822 2.054047e-04 7.168831
698778 rs1864453 2_105 1.251599e-01 3612.780 4.386490e-04 7.207792
698770 rs2033315 2_105 5.844195e-02 3609.583 2.046408e-04 7.064935
698781 rs6707162 2_105 1.730083e-02 3603.368 6.047640e-05 7.090909
698782 rs6735680 2_105 1.150635e-02 3602.875 4.021584e-05 7.077922
698771 rs2033314 2_105 1.165286e-02 3602.717 4.072611e-05 7.155844
698773 rs28485554 2_105 2.399129e-03 3600.749 8.380248e-06 7.000000
698783 rs4972703 2_105 1.000000e+00 3592.885 3.485409e-03 -0.784267
698804 rs10803884 2_105 3.412607e-05 3550.073 1.175260e-07 7.285714
698812 rs6738901 2_105 6.033312e-05 3535.783 2.069435e-07 -7.272727
698797 rs12466643 2_105 1.495366e-05 3532.253 5.124007e-08 7.272727
698828 rs35368253 2_105 1.910799e-05 3515.570 6.516601e-08 -7.256410
698814 rs10197521 2_105 2.167801e-08 3505.736 7.372403e-11 -6.547619
698816 rs34661753 2_105 1.912728e-06 3466.123 6.431433e-09 -7.076923
698767 rs7590328 2_105 1.204450e-07 3454.423 4.036218e-10 6.784810
183948 rs1906615 4_72 1.000000e+00 3299.177 3.200487e-03 45.160494
698765 rs6433497 2_105 2.090339e-11 2907.446 5.895746e-14 6.345679
698766 rs2115874 2_105 2.801248e-11 2905.297 7.895008e-14 6.419753
698758 rs1430185 2_105 1.876388e-12 2842.067 5.173296e-15 6.185185
698745 rs1991601 2_105 5.335732e-13 2821.002 1.460185e-15 5.950617
703494 rs56204325 3_9 7.189264e-01 2763.521 1.927337e-03 7.865672
703475 rs1969154 3_9 3.789176e-01 2761.449 1.015061e-03 7.850746
703474 rs6799179 3_9 3.766987e-01 2761.418 1.009106e-03 7.850746
703484 rs12714880 3_9 1.905204e-01 2760.752 5.102457e-04 7.820896
703442 rs6763619 3_9 6.794745e-03 2742.502 1.807717e-05 7.776119
703441 rs13320486 3_9 6.774412e-03 2742.480 1.802293e-05 7.776119
703443 rs9883561 3_9 5.623830e-04 2740.038 1.494855e-06 7.676471
703469 rs9821066 3_9 3.249060e-05 2729.436 8.602823e-08 7.588235
703464 rs9872103 3_9 1.785730e-04 2728.262 4.726201e-07 7.686567
703465 rs9871991 3_9 3.800932e-04 2727.319 1.005626e-06 7.716418
703470 rs9877165 3_9 4.469283e-05 2727.313 1.182451e-07 7.626866
703476 rs1985428 3_9 3.173254e-05 2727.176 8.395150e-08 7.611940
703489 rs114415025 3_9 1.000000e+00 2723.925 2.642443e-03 1.219251
703461 rs6791647 3_9 2.233448e-05 2720.842 5.895080e-08 7.611940
703456 rs4447735 3_9 3.120521e-05 2720.726 8.236113e-08 7.626866
703462 rs6767504 3_9 7.609822e-06 2717.065 2.005788e-08 7.597015
703459 rs4321514 3_9 7.424475e-06 2716.792 1.956737e-08 7.597015
703457 rs4299468 3_9 7.118141e-06 2716.475 1.875783e-08 7.597015
703452 rs3901665 3_9 1.258296e-05 2715.352 3.314511e-08 7.626866
703488 rs56082700 3_9 0.000000e+00 2702.262 0.000000e+00 2.696970
703471 rs9822382 3_9 0.000000e+00 2678.591 0.000000e+00 4.277228
703447 rs9870070 3_9 0.000000e+00 2676.505 0.000000e+00 4.516129
703445 rs9850214 3_9 0.000000e+00 2676.317 0.000000e+00 4.483871
703448 rs9850227 3_9 0.000000e+00 2675.871 0.000000e+00 4.397849
703558 rs3732675 3_9 1.173251e-08 2674.016 3.043446e-11 7.735294
703446 rs9850480 3_9 0.000000e+00 2664.144 0.000000e+00 4.505376
703492 rs11706068 3_9 2.610084e-06 2600.801 6.585245e-09 7.970588SNPs with highest PVE
id region_tag susie_pip mu2 PVE z
698783 rs4972703 2_105 1.00000000 3592.8850 0.0034854089 -0.7842670
183948 rs1906615 4_72 1.00000000 3299.1775 0.0032004872 45.1604938
698793 rs1367220 2_105 0.90278725 3624.4736 0.0031742475 7.2207792
703489 rs114415025 3_9 1.00000000 2723.9251 0.0026424427 1.2192513
703494 rs56204325 3_9 0.71892638 2763.5212 0.0019273369 7.8656716
768375 rs61937778 12_35 1.00000000 1898.7373 0.0018419393 -1.3056995
272791 rs111990232 6_59 1.00000000 1672.2132 0.0016221913 0.5392670
183953 rs7440714 4_72 1.00000000 1498.4064 0.0014535837 -9.2183406
272788 rs371814 6_59 0.88875486 1684.1863 0.0014520532 6.1911765
28638 rs7536152 1_75 1.00000000 1439.6465 0.0013965815 -6.4626866
703515 rs4642101 3_9 0.71504872 1969.7326 0.0013663229 10.2318841
28637 rs12404927 1_75 1.00000000 1404.5510 0.0013625359 -1.5517241
768315 rs2860482 12_35 0.72039239 1945.5816 0.0013596558 -7.1052632
232614 rs199992924 5_68 0.99677991 1308.3614 0.0012651366 -0.6309524
232607 rs4073838 5_68 0.89071507 1336.8900 0.0011551674 -5.9545455
768370 rs7313074 12_35 0.59547601 1953.4234 0.0011284208 -6.9868421
728978 rs201862093 7_48 1.00000000 1114.3649 0.0010810302 -0.8625000
703475 rs1969154 3_9 0.37891760 2761.4487 0.0010150611 7.8507463
703474 rs6799179 3_9 0.37669868 2761.4183 0.0010091059 7.8507463
729019 rs112661041 7_48 0.92465841 1098.8711 0.0009856858 4.6532258
765251 rs76106073 10_44 1.00000000 836.8554 0.0008118220 0.6572238
698789 rs10168156 2_105 0.22653976 3615.0005 0.0007944439 7.2337662
705484 rs9830653 3_84 0.94971640 834.6821 0.0007689985 -0.9344262
768373 rs4759256 12_35 0.40562812 1952.8889 0.0007684507 -6.9736842
592256 rs62056842 17_28 1.00000000 764.0781 0.0007412218 1.1269036
272792 rs384318 6_59 0.37973072 1682.6223 0.0006198303 6.1029412
728888 rs12154789 7_48 0.51476523 1098.6922 0.0005486504 4.4923077
703514 rs7650482 3_9 0.28023466 1973.5020 0.0005365002 10.1571429
703484 rs12714880 3_9 0.19052042 2760.7520 0.0005102457 7.8208955
121514 rs12330500 3_40 0.99969702 506.3653 0.0004910693 0.5641026
704796 rs199808025 3_84 0.56221627 819.6038 0.0004470106 0.3170732
698778 rs1864453 2_105 0.12515989 3612.7802 0.0004386490 7.2077922
272793 rs1145714 6_59 0.26668394 1679.0994 0.0004343939 6.1029412
121517 rs6924 3_40 0.82385812 510.0248 0.0004076187 4.2133333
785055 rs8005417 14_9 0.99999767 418.1701 0.0004056602 0.9863946
785061 rs8011559 14_9 0.96440477 426.2857 0.0003988142 5.6913580
232606 rs4235764 5_68 0.29404637 1335.1711 0.0003808581 -5.8787879
768310 rs7978685 12_35 0.19327209 1942.9081 0.0003642770 -7.0657895
556241 rs74022964 15_35 1.00000000 340.3300 0.0003301495 12.5777778
698794 rs1367219 2_105 0.08971134 3615.4774 0.0003146469 7.1038961
232609 rs4235768 5_68 0.24023863 1335.2967 0.0003111939 -5.8030303
272750 rs9444476 6_59 0.19310251 1660.7317 0.0003110984 -6.3088235
28731 rs34515871 1_76 1.00000000 296.9840 0.0002881002 17.0000000
272775 rs9444488 6_59 0.17207131 1665.5818 0.0002780256 -6.2647059
556238 rs140798119 15_35 1.00000000 282.6223 0.0002741680 3.9950739
183979 rs186546224 4_72 0.99999999 278.2802 0.0002699558 -6.8398876
183968 rs4631108 4_72 0.98588526 278.7291 0.0002665748 -17.6376812
323204 rs28557111 7_70 0.99999953 268.5095 0.0002604773 13.6818182
733889 rs62643683 8_21 0.99999999 262.9862 0.0002551193 0.8007519
183920 rs1823291 4_72 0.94438487 275.3827 0.0002522877 -19.4520548SNPs with largest z scores
id region_tag susie_pip mu2 PVE z
183948 rs1906615 4_72 1.000000e+00 3299.1775 3.200487e-03 45.16049
183949 rs75725917 4_72 0.000000e+00 1501.2534 0.000000e+00 42.33663
183947 rs1906611 4_72 0.000000e+00 1386.7531 0.000000e+00 40.97143
183946 rs28521134 4_72 0.000000e+00 1323.8641 0.000000e+00 40.22772
183942 rs10019689 4_72 0.000000e+00 1314.7532 0.000000e+00 40.11000
183943 rs76013973 4_72 0.000000e+00 1309.8604 0.000000e+00 40.04902
183945 rs12639820 4_72 0.000000e+00 1308.0495 0.000000e+00 40.03922
183941 rs12647393 4_72 0.000000e+00 1303.9357 0.000000e+00 39.98020
183944 rs74496596 4_72 0.000000e+00 1284.8290 0.000000e+00 39.75728
183940 rs12647316 4_72 0.000000e+00 1271.3853 0.000000e+00 39.55882
183939 rs4529121 4_72 0.000000e+00 1275.2573 0.000000e+00 39.55340
183933 rs12650829 4_72 0.000000e+00 605.3700 0.000000e+00 31.54444
183956 rs3866831 4_72 0.000000e+00 1596.6468 0.000000e+00 -30.10000
183955 rs6533530 4_72 0.000000e+00 1580.2990 0.000000e+00 -29.91429
183938 rs12644107 4_72 0.000000e+00 465.5759 0.000000e+00 25.98851
183936 rs2723318 4_72 0.000000e+00 813.2565 0.000000e+00 -25.45833
183931 rs2218698 4_72 0.000000e+00 771.3648 0.000000e+00 -25.09589
183934 rs2197814 4_72 0.000000e+00 772.0146 0.000000e+00 24.59722
183932 rs1448799 4_72 0.000000e+00 770.9787 0.000000e+00 24.56944
183930 rs112927894 4_72 0.000000e+00 741.1342 0.000000e+00 24.50685
183920 rs1823291 4_72 9.443849e-01 275.3827 2.522877e-04 -19.45205
183924 rs2723296 4_72 5.561070e-02 266.6973 1.438757e-05 -19.02740
183929 rs11724067 4_72 0.000000e+00 654.4966 0.000000e+00 -18.94059
183923 rs2044674 4_72 4.429420e-06 242.9736 1.044038e-09 18.58108
183968 rs4631108 4_72 9.858853e-01 278.7291 2.665748e-04 -17.63768
183967 rs1906613 4_72 1.411474e-02 268.6140 3.678003e-06 17.34783
28731 rs34515871 1_76 1.000000e+00 296.9840 2.881002e-04 17.00000
423415 rs60469668 10_66 1.000000e+00 171.3926 1.662657e-04 16.96471
183928 rs13111704 4_72 0.000000e+00 700.2351 0.000000e+00 -16.91743
28734 rs12058931 1_76 2.023295e-04 220.3706 4.325369e-08 16.54054
183952 rs4124159 4_72 0.000000e+00 1664.4211 0.000000e+00 -16.14414
183950 rs1906606 4_72 0.000000e+00 1659.0494 0.000000e+00 -16.02703
183957 rs4032974 4_72 0.000000e+00 1649.6039 0.000000e+00 -15.86726
183977 rs17513625 4_72 0.000000e+00 196.2481 0.000000e+00 15.71130
183954 rs10006881 4_72 0.000000e+00 1641.6919 0.000000e+00 -15.68750
423411 rs12572965 10_66 2.787622e-04 132.8475 3.592507e-08 15.27059
423410 rs56965730 10_66 2.796755e-04 131.7056 3.573296e-08 15.21176
183922 rs12642151 4_72 7.894574e-12 227.0161 1.738585e-15 14.14286
423413 rs7094488 10_66 9.999961e-01 105.1201 1.019752e-04 14.10606
672306 rs577676 1_84 4.329934e-04 124.1225 5.213653e-08 -13.77612
323204 rs28557111 7_70 9.999995e-01 268.5095 2.604773e-04 13.68182
672415 rs680084 1_84 6.024752e-04 136.4064 7.972312e-08 -13.53731
672386 rs608930 1_84 1.253762e-03 138.0822 1.679436e-07 -13.52239
672422 rs629234 1_84 5.624740e-04 135.5991 7.398942e-08 -13.52239
672340 rs598993 1_84 9.849966e-04 137.8588 1.317285e-07 -13.51515
672343 rs541557 1_84 9.796191e-04 137.8182 1.309707e-07 -13.51515
672429 rs525489 1_84 1.190958e-03 137.5496 1.589156e-07 -13.49254
672430 rs503706 1_84 1.177181e-03 137.4686 1.569846e-07 -13.49254
672350 rs539045 1_84 8.984718e-04 136.7722 1.192100e-07 -13.48485
672356 rs580487 1_84 8.877917e-04 136.6820 1.177153e-07 -13.48485Gene set enrichment for genes with PIP>0.8
Welcome to enrichR
Checking connection ... Enrichr ... Connection is Live!
FlyEnrichr ... Connection is available!
WormEnrichr ... Connection is available!
YeastEnrichr ... Connection is available!
FishEnrichr ... Connection is available![1] 60Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
[1] Term Overlap Adjusted.P.value Genes
<0 rows> (or 0-length row.names)
[1] "GO_Cellular_Component_2021"
Term Overlap Adjusted.P.value Genes
1 sarcolemma (GO:0042383) 3/52 0.04598333 SSPN;BVES;PLEC
[1] "GO_Molecular_Function_2021"[1] Term Overlap Adjusted.P.value Genes
<0 rows> (or 0-length row.names)GPRIN3 gene(s) from the input list not found in DisGeNET CURATEDGCN1 gene(s) from the input list not found in DisGeNET CURATEDSEC23IP gene(s) from the input list not found in DisGeNET CURATEDC8orf48 gene(s) from the input list not found in DisGeNET CURATEDADSS gene(s) from the input list not found in DisGeNET CURATEDPWP1 gene(s) from the input list not found in DisGeNET CURATEDSPNS1 gene(s) from the input list not found in DisGeNET CURATEDC9orf43 gene(s) from the input list not found in DisGeNET CURATEDVPS37B gene(s) from the input list not found in DisGeNET CURATEDLINC01314 gene(s) from the input list not found in DisGeNET CURATEDRAB1A gene(s) from the input list not found in DisGeNET CURATEDPAFAH1B2 gene(s) from the input list not found in DisGeNET CURATEDSRL gene(s) from the input list not found in DisGeNET CURATEDCMTM5 gene(s) from the input list not found in DisGeNET CURATEDTOMM5 gene(s) from the input list not found in DisGeNET CURATEDSSSCA1 gene(s) from the input list not found in DisGeNET CURATEDGMCL1 gene(s) from the input list not found in DisGeNET CURATEDSTK11IP gene(s) from the input list not found in DisGeNET CURATEDJAM2 gene(s) from the input list not found in DisGeNET CURATEDZSWIM8 gene(s) from the input list not found in DisGeNET CURATEDCTNNAL1 gene(s) from the input list not found in DisGeNET CURATEDMICU2 gene(s) from the input list not found in DisGeNET CURATEDLINC00964 gene(s) from the input list not found in DisGeNET CURATEDWASHC2C gene(s) from the input list not found in DisGeNET CURATEDMRPS31 gene(s) from the input list not found in DisGeNET CURATEDFAM46C gene(s) from the input list not found in DisGeNET CURATED Description FDR Ratio BgRatio
89 Paroxysmal atrial fibrillation 1.518444e-13 13/34 156/9703
174 Persistent atrial fibrillation 1.518444e-13 13/34 156/9703
192 familial atrial fibrillation 1.518444e-13 13/34 156/9703
6 Atrial Fibrillation 1.590688e-13 13/34 160/9703
62 Congenital retrognathism 2.170801e-02 1/34 1/9703
91 Female Pseudohermaphroditism 2.170801e-02 1/34 1/9703
98 Toxic effect of heavy metal 2.170801e-02 1/34 1/9703
118 Epidermolysis bullosa simplex, Ogna type 2.170801e-02 1/34 1/9703
144 Glucose Metabolism Disorders 2.170801e-02 1/34 1/9703
158 Glucocorticoid Receptor Deficiency 2.170801e-02 1/34 1/9703******************************************
* *
* Welcome to WebGestaltR ! *
* *
******************************************Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...Warning in oraEnrichment(interestGeneList, referenceGeneList, geneSet, minNum =
minNum, : No significant gene set is identified based on FDR 0.05!
NULLPIP Manhattan Plot
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──✔ tidyr 1.1.4 ✔ dplyr 1.0.7
✔ readr 2.1.1 ✔ stringr 1.4.0
✔ purrr 0.3.4 ✔ forcats 0.5.1── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ tidyr::extract() masks disgenet2r::extract()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()Warning: ggrepel: 27 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
| Version | Author | Date |
|---|---|---|
| 4106919 | sq-96 | 2021-12-24 |
Locus Plots - 2_46
Locus Plots - 5_103
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[5] readr_2.1.1 tidyr_1.1.4 tidyverse_1.3.1 tibble_3.1.6
[9] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0 cowplot_1.0.0
[13] ggplot2_3.3.5 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.2 lubridate_1.8.0 bit64_4.0.5 doParallel_1.0.16
[5] httr_1.4.2 rprojroot_2.0.2 tools_3.6.1 backports_1.4.1
[9] doRNG_1.8.2 utf8_1.2.2 R6_2.5.1 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.3 ggrastr_1.0.1
[17] tidyselect_1.1.1 bit_4.0.4 curl_4.3.2 compiler_3.6.1
[21] git2r_0.26.1 cli_3.1.0 rvest_1.0.2 Cairo_1.5-12.2
[25] xml2_1.3.3 labeling_0.4.2 scales_1.1.1 apcluster_1.4.8
[29] digest_0.6.29 rmarkdown_2.11 svglite_1.2.2 pkgconfig_2.0.3
[33] htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 highr_0.9
[37] rlang_0.4.12 readxl_1.3.1 rstudioapi_0.13 RSQLite_2.2.8
[41] jquerylib_0.1.4 farver_2.1.0 generics_0.1.1 jsonlite_1.7.2
[45] vroom_1.5.7 magrittr_2.0.1 Matrix_1.2-18 ggbeeswarm_0.6.0
[49] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0 gdtools_0.1.9
[53] lifecycle_1.0.1 stringi_1.7.6 whisker_0.3-2 yaml_2.2.1
[57] plyr_1.8.6 grid_3.6.1 blob_1.2.2 ggrepel_0.9.1
[61] parallel_3.6.1 promises_1.0.1 crayon_1.4.2 lattice_0.20-38
[65] haven_2.4.3 hms_1.1.1 knitr_1.36 pillar_1.6.4
[69] igraph_1.2.10 rjson_0.2.20 rngtools_1.5.2 reshape2_1.4.4
[73] codetools_0.2-16 reprex_2.0.1 glue_1.5.1 evaluate_0.14
[77] data.table_1.14.2 modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0
[81] httpuv_1.5.1 foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0
[85] assertthat_0.2.1 cachem_1.0.6 xfun_0.29 broom_0.7.10
[89] later_0.8.0 iterators_1.0.13 beeswarm_0.2.3 memoise_2.0.1
[93] ellipsis_0.3.2